# HG changeset patch
# User tduigou
# Date 1644417426 0
# Node ID 47bb93e7832b516190afbd1d2ebafd2ecde761ea
# Parent  8d16a0f08d0a11157d815e4a5b9d22f0a147f262
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

diff -r 8d16a0f08d0a -r 47bb93e7832b rpextractsink.xml
--- a/rpextractsink.xml	Tue Jan 11 10:26:50 2022 +0000
+++ b/rpextractsink.xml	Wed Feb 09 14:37:06 2022 +0000
@@ -1,29 +1,34 @@
-<tool id="rpextractsink" name="Sink from SBML" version="5.11.1" profile="19.09">
+<tool id="rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@" profile="19.09">
     <description>Generate the RetroPath2.0 sink file from an SBML input</description>
+    <macros>
+        <token name="@TOOL_VERSION@">5.12.1</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="5.11.1">rptools</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
     </requirements>
     <stdio>
-		<regex match="Could not retreive any species in the compartment" level="fatal" />
-	</stdio>
+        <regex match="Could not retreive any species in the compartment" level="fatal" />
+    </stdio>
     <command detect_errors="exit_code"><![CDATA[
         python -m rptools.rpextractsink
             '$input'
             '$sink'
-            --compartment_id '$adv.compartment_id'
+            --compartment_id '$compartment_id'
         #if str($adv.remove_dead_end) == "true":
             --remove_dead_end
         #end if
     ]]></command>
     <inputs>
         <param name="input" type="data" format="xml" optional="false" label="Strain" />
+        <param name="compartment_id" type="text" value="c" label="SBML compartment ID" >
+            <validator type="empty_field" message="SBML compartment ID is required"/>
+        </param>
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="compartment_id" type="text" value="c" label="SBML compartment ID" />
             <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" />
         </section>
     </inputs>
     <outputs>
-        <data name="sink" format="csv" label="${tool.name} - ${input.name}" />
+        <data name="sink" format="csv" metadata_source="input" label="Sink - ${input.name}" />
     </outputs>
     <tests>
         <test>
@@ -39,7 +44,7 @@
 
 Sink refers to the collection of chemical species used by the restrosynthesis algorithm of RetroPath2.0 to finish metabolic route exploration. This tool uses an SBML file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytoplasm, Golgi apparatus, nucleus, etc) and uses its MIRIAM annotation to find their InChI structures. You can use "Remove dead-end metabolites using FVA evaluation? to conduct Flux Variability Analysis to remove metabolites that lack the requisite flux that would account for their production or consumption within the metabolic network.
 
-In the advanced options, one can specify the compartment from which the tool will extract the chemical species. The default is MNXC3, the MetaNetX code for the cytoplasm. If the user wishes to upload an SBML file from another source, then this value must be changed.
+In the advanced options, one can specify the compartment from which the tool will extract the chemical species. The default is 'c', the BiGG code for the cytoplasm. If the user wishes to upload an SBML file from another source, then this value must be changed.
 
 The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input.
 
@@ -50,11 +55,11 @@
 Required:
 
 * **input_sbml**\ : (string) Path to the input SBML file
+* **compartment_id**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models
 
 Advanced options:
 
 * **remove_dead_end**\ : (boolean, default: True) Perform FVA evaluation to remove dead end metabolites
-* **compartment_id**\ : (string, default: MNXC3) Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files
 
 Output
 ------
@@ -69,7 +74,7 @@
 Version
 ----------
 
-5.11.1
+5.12.1
 
 Authors
 -------